An unsigned letter from the foreign affairs ministry declared the WHO representative Dr Walter Kazadi Mulombo and three others as "persona non grata" and gave them 48 hours to leave the country.
The other three are Prof Tarzy Daniel, Dr Ruhana Mirindi Bisimwa and Dr Jean Pierre Murunda.
The ministry did not give any reason for asking the officials to leave the country.
The Burundi government is being criticised for organising elections amid the coronavirus pandemic.
Campaign rallies are ongoing ahead of the election which would be held on May 20, 2020. At these rallies, little or no measures are put in place to curb the spread of the disease, causing fear of its imminent spread.
In a press briefing on Wednesday, the International Crisis Group said the Burundi government is working in denial, questioning the number of coronavirus cases the country has announced.
The country has reported 15 cases so far including one death.
According to the BBC, Burundi Foreign Affairs Minister Ezechiel Nibigira did not deny or confirm the letter when he was reached.
But a source at the ministry confirmed its authenticity to the media house.